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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene

pdxH

Organism
Parvibaculum lavamentivorans (strain DS-1 / DSM 13023 / NCIMB 13966)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP).UniRule annotation

Catalytic activityi

Pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + H2O2.UniRule annotation
Pyridoxine 5'-phosphate + O2 = pyridoxal 5'-phosphate + H2O2.UniRule annotation

Cofactori

FMNUniRule annotationNote: Binds 1 FMN per subunit.UniRule annotation

Pathway: B6 vitamer interconversion

This protein is involved in step 1 of the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Pyridoxine/pyridoxamine 5'-phosphate oxidase (pdxH)
This subpathway is part of the pathway B6 vitamer interconversion, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate, the pathway B6 vitamer interconversion and in Cofactor biosynthesis.

Pathway: B6 vitamer interconversion

This protein is involved in step 1 of the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxine 5'-phosphate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Pyridoxine/pyridoxamine 5'-phosphate oxidase (pdxH)
This subpathway is part of the pathway B6 vitamer interconversion, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxine 5'-phosphate, the pathway B6 vitamer interconversion and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei55 – 551FMNUniRule annotation
Binding sitei58 – 581FMN; via amide nitrogenUniRule annotation
Binding sitei60 – 601SubstrateUniRule annotation
Binding sitei77 – 771FMNUniRule annotation
Binding sitei117 – 1171SubstrateUniRule annotation
Binding sitei121 – 1211SubstrateUniRule annotation
Binding sitei125 – 1251SubstrateUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi70 – 712FMNUniRule annotation
Nucleotide bindingi134 – 1352FMNUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Pyridoxine biosynthesis

Keywords - Ligandi

Flavoprotein, FMN

Enzyme and pathway databases

BioCyciPLAV402881:GHQA-800-MONOMER.
UniPathwayiUPA00190; UER00304.
UPA00190; UER00305.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxine/pyridoxamine 5'-phosphate oxidaseUniRule annotation (EC:1.4.3.5UniRule annotation)
Alternative name(s):
PNP/PMP oxidaseUniRule annotation
Short name:
PNPOxUniRule annotation
Pyridoxal 5'-phosphate synthaseUniRule annotation
Gene namesi
Name:pdxHUniRule annotation
Ordered Locus Names:Plav_0790
OrganismiParvibaculum lavamentivorans (strain DS-1 / DSM 13023 / NCIMB 13966)
Taxonomic identifieri402881 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhodobiaceaeParvibaculum
ProteomesiUP000006377 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 208208Pyridoxine/pyridoxamine 5'-phosphate oxidasePRO_0000335794Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi402881.Plav_0790.

Structurei

3D structure databases

ProteinModelPortaliA7HR80.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni185 – 1873Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the pyridoxamine 5'-phosphate oxidase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
KOiK00275.
OMAiEYTARYA.
OrthoDBiEOG60KN2Z.

Family and domain databases

Gene3Di2.30.110.10. 1 hit.
HAMAPiMF_01629. PdxH.
InterProiIPR000659. Pyridox_Oxase.
IPR019740. Pyridox_Oxase_CS.
IPR011576. Pyridox_Oxase_FMN-bd.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN-bd.
[Graphical view]
PANTHERiPTHR10851. PTHR10851. 1 hit.
PfamiPF10590. PNPOx_C. 1 hit.
PF01243. Pyridox_oxidase. 1 hit.
[Graphical view]
PIRSFiPIRSF000190. Pyd_amn-ph_oxd. 1 hit.
SUPFAMiSSF50475. SSF50475. 1 hit.
TIGRFAMsiTIGR00558. pdxH. 1 hit.
PROSITEiPS01064. PYRIDOX_OXIDASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A7HR80-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNDVTTATDE SGIFTSEDPI ALFHEWMELA RAKEPEDANA MALATADASG
60 70 80 90 100
FPDVRMVLLK EADARGFVFY TNLESAKGLE LKENSRAALC FHWKSLRRQV
110 120 130 140 150
RVRGDVIPVS KEEADAYFAT RARDSQIGAW ASKQSRPLAG RFELEKQVAV
160 170 180 190 200
FAAKFGVSRV PRPDHWSGFR VVPRHIEFWR DRPFRLHDRL VFEREKPAEA

WRTKKLFP
Length:208
Mass (Da):23,851
Last modified:September 11, 2007 - v1
Checksum:i237F37D51B34AC11
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000774 Genomic DNA. Translation: ABS62413.1.
RefSeqiWP_012109663.1. NC_009719.1.
YP_001412070.1. NC_009719.1.

Genome annotation databases

EnsemblBacteriaiABS62413; ABS62413; Plav_0790.
KEGGipla:Plav_0790.
PATRICi22863148. VBIParLav90819_0817.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000774 Genomic DNA. Translation: ABS62413.1.
RefSeqiWP_012109663.1. NC_009719.1.
YP_001412070.1. NC_009719.1.

3D structure databases

ProteinModelPortaliA7HR80.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi402881.Plav_0790.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABS62413; ABS62413; Plav_0790.
KEGGipla:Plav_0790.
PATRICi22863148. VBIParLav90819_0817.

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
KOiK00275.
OMAiEYTARYA.
OrthoDBiEOG60KN2Z.

Enzyme and pathway databases

UniPathwayiUPA00190; UER00304.
UPA00190; UER00305.
BioCyciPLAV402881:GHQA-800-MONOMER.

Family and domain databases

Gene3Di2.30.110.10. 1 hit.
HAMAPiMF_01629. PdxH.
InterProiIPR000659. Pyridox_Oxase.
IPR019740. Pyridox_Oxase_CS.
IPR011576. Pyridox_Oxase_FMN-bd.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN-bd.
[Graphical view]
PANTHERiPTHR10851. PTHR10851. 1 hit.
PfamiPF10590. PNPOx_C. 1 hit.
PF01243. Pyridox_oxidase. 1 hit.
[Graphical view]
PIRSFiPIRSF000190. Pyd_amn-ph_oxd. 1 hit.
SUPFAMiSSF50475. SSF50475. 1 hit.
TIGRFAMsiTIGR00558. pdxH. 1 hit.
PROSITEiPS01064. PYRIDOX_OXIDASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Complete genome sequence and annotation of Parvibaculum lavamentivorans DS-1."
    Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E., Tice H., Pitluck S., Saunders E., Brettin T., Bruce D., Detter J.C., Han C., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Richardson P.
    Submitted (JUL-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DS-1 / DSM 13023 / NCIMB 13966.

Entry informationi

Entry nameiPDXH_PARL1
AccessioniPrimary (citable) accession number: A7HR80
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 20, 2008
Last sequence update: September 11, 2007
Last modified: April 29, 2015
This is version 57 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.